In 1996 Paquette drew two miniseries adapted from the TV series Space: Above and Beyond, written by Roy Thomas, for Topps Comics. The following year he and Thomas reunited to draw Xena: Warrior Princess: Year One for Topps.

In 1997 Paquette drew two issues of JLA Secret Files, his first work on the Justice League of America. He would return to those characters in 1998 with JLA: Tomorrow Woman and "Madmen and Mudbaths", one of the stories in the 1999 anthology book JLA 80-Page Giant #2. From 1998 to 1999, Paquette drew nine issues of Wonder Woman for DC Comics.Clément Sauvé was his assistant on background on a wide number of issues from 2000 to 2002. From 2000 to 2001, Yanick drew ten issues of Gambit.

Paquette was the regular artist on Ultimate X-Men from February 2007 to January 2008, and for the first five issues of Young X-Men in 2008.He drew first five issues of Young X-Men in 2008. He later supplied the art for Batman: The Return of Bruce Wayne #3 (August 2010),and launched Batman Incorporated, which was written by Grant Morrison.

In September 2011, DC Comics cancelled all their monthly superhero comics and rebooted their entire continuity with 52 new monthly series in an initiative called The New 52. Among the new titles was a Swamp Thing series whose initial story arcs were written by Scott Snyder and drawn by Paquette. His work on the series garnered him a nomination for the 2013 Shuster Awards for Best Artist and Best Cover Artist.